SMTL ID : 5ein.1

Crystal structure of C148A mutant of LysY from Thermus thermophilus in complex with NADP+ and LysW-gamma-aminoadipic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

hetero-4-2-mer

Ligands

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 29 residues within 4Å: Chain A: G.10, A.11, S.12, G.13, Y.14, A.15, S.36, R.37, R.38, A.74, L.75, P.76, H.77, V.79, L.97, S.98, R.102, A.148, S.180, A.181, G.183, A.184, N.312, L.313, G.316, T.317 Chain C: E.54 Ligands: FMT.6, FMT.8 35 PLIP interactions: 35 interactions with chain A Hydrophobic interactions: A:A.148, A:T.317 Hydrogen bonds: A:G.10, A:S.12, A:S.12, A:G.13, A:Y.14, A:A.15, A:R.37, A:R.38, A:L.75, A:S.180, A:A.184, A:N.312 Water bridges: A:G.10, A:G.10, A:S.12, A:G.16, A:R.37, A:R.37, A:R.37, A:R.38, A:R.38, A:H.77, A:H.77, A:E.83, A:Y.87, A:A.99, A:R.102, A:E.185, A:E.185 Salt bridges: A:R.37, A:R.38 pi-Cation interactions: A:R.37, A:R.37 NAP.14: 26 residues within 4Å: Chain B: G.10, A.11, S.12, G.13, Y.14, A.15, S.36, R.37, R.38, A.74, L.75, P.76, H.77, V.79, L.97, S.98, R.102, A.148, S.180, A.181, G.183, A.184, N.312, L.313, G.316, T.317 27 PLIP interactions: 27 interactions with chain B Hydrophobic interactions: B:A.148, B:T.317 Hydrogen bonds: B:G.10, B:S.12, B:S.12, B:G.13, B:Y.14, B:A.15, B:R.37, B:R.38, B:L.75, B:S.180, B:A.184, B:N.312 Water bridges: B:G.10, B:G.16, B:T.35, B:R.38, B:R.38, B:R.38, B:R.38, B:H.77, B:A.99, B:R.102, B:E.185 Salt bridges: B:R.37 pi-Cation interactions: B:R.37 NAP.27: 29 residues within 4Å: Chain D: G.10, A.11, S.12, G.13, Y.14, A.15, S.36, R.37, R.38, A.74, L.75, P.76, H.77, V.79, L.97, S.98, R.102, A.148, S.180, A.181, G.183, A.184, N.312, L.313, G.316, T.317 Chain F: E.54 Ligands: FMT.32, FMT.34 33 PLIP interactions: 33 interactions with chain D Hydrophobic interactions: D:A.148, D:T.317 Hydrogen bonds: D:G.10, D:S.12, D:S.12, D:G.13, D:Y.14, D:A.15, D:R.37, D:R.38, D:L.75, D:S.180, D:A.184, D:N.312 Water bridges: D:G.10, D:G.10, D:S.12, D:G.16, D:R.37, D:R.37, D:R.37, D:R.38, D:R.38, D:H.77, D:H.77, D:E.83, D:A.99, D:R.102, D:E.185 Salt bridges: D:R.37, D:R.38 pi-Cation interactions: D:R.37, D:R.37 NAP.40: 26 residues within 4Å: Chain E: G.10, A.11, S.12, G.13, Y.14, A.15, S.36, R.37, R.38, A.74, L.75, P.76, H.77, V.79, L.97, S.98, R.102, A.148, S.180, A.181, G.183, A.184, N.312, L.313, G.316, T.317 28 PLIP interactions: 28 interactions with chain E Hydrophobic interactions: E:A.148, E:T.317 Hydrogen bonds: E:G.10, E:S.12, E:S.12, E:G.13, E:Y.14, E:A.15, E:R.37, E:R.38, E:L.75, E:S.180, E:A.184, E:N.312 Water bridges: E:G.10, E:G.16, E:T.35, E:R.38, E:R.38, E:R.38, E:R.38, E:H.77, E:A.99, E:R.102, E:E.185, E:E.185 Salt bridges: E:R.37 pi-Cation interactions: E:R.37

46 x FMT: FORMIC ACID(Non-functional Binders)

FMT.2: 2 residues within 4Å: Chain A: R.134, E.135 Ligand excluded by PLIP FMT.3: 4 residues within 4Å: Chain A: R.134, G.263, P.265, E.333 Ligand excluded by PLIP FMT.4: 5 residues within 4Å: Chain A: H.77, G.78, D.100, Y.109, Y.113 Ligand excluded by PLIP FMT.5: 4 residues within 4Å: Chain A: P.62, E.63, R.86, Y.87 Ligand excluded by PLIP FMT.6: 4 residues within 4Å: Chain A: A.181, R.208 Chain C: E.54 Ligands: NAP.1 Ligand excluded by PLIP FMT.7: 2 residues within 4Å: Chain A: S.88 Ligands: FMT.12 Ligand excluded by PLIP FMT.8: 4 residues within 4Å: Chain A: R.37, P.76, V.79 Ligands: NAP.1 Ligand excluded by PLIP FMT.9: 3 residues within 4Å: Chain A: G.53, R.54 Chain D: D.338 Ligand excluded by PLIP FMT.10: 4 residues within 4Å: Chain A: E.250, W.254, F.295, E.296 Ligand excluded by PLIP FMT.11: 5 residues within 4Å: Chain A: V.270, K.271, Q.272, R.278, Y.279 Ligand excluded by PLIP FMT.12: 3 residues within 4Å: Chain A: S.88, W.142 Ligands: FMT.7 Ligand excluded by PLIP FMT.13: 2 residues within 4Å: Chain A: L.269, K.271 Ligand excluded by PLIP FMT.15: 6 residues within 4Å: Chain B: N.149, I.177, A.181, Y.202, H.207, A.227 Ligand excluded by PLIP FMT.16: 5 residues within 4Å: Chain B: K.138, N.326, V.327, G.330, W.331 Ligand excluded by PLIP FMT.17: 2 residues within 4Å: Chain B: R.134, E.333 Ligand excluded by PLIP FMT.18: 4 residues within 4Å: Chain B: K.104, V.126, Y.127, Y.133 Ligand excluded by PLIP FMT.19: 6 residues within 4Å: Chain B: V.270, H.277, Y.279, D.281, F.284 Chain E: P.49 Ligand excluded by PLIP FMT.20: 4 residues within 4Å: Chain B: R.283, F.284, L.342, P.344 Ligand excluded by PLIP FMT.21: 7 residues within 4Å: Chain B: P.168, T.169, P.170, I.171, P.221, E.222 Ligands: FMT.24 Ligand excluded by PLIP FMT.22: 5 residues within 4Å: Chain A: E.298 Chain B: Y.112, G.206, H.207, T.210 Ligand excluded by PLIP FMT.23: 4 residues within 4Å: Chain B: Y.133, N.216, L.217, P.218 Ligand excluded by PLIP FMT.24: 5 residues within 4Å: Chain B: L.161, P.168, G.219, P.221 Ligands: FMT.21 Ligand excluded by PLIP FMT.25: 1 residues within 4Å: Chain B: E.222 Ligand excluded by PLIP FMT.28: 2 residues within 4Å: Chain D: R.134, E.135 Ligand excluded by PLIP FMT.29: 4 residues within 4Å: Chain D: R.134, G.263, P.265, E.333 Ligand excluded by PLIP FMT.30: 5 residues within 4Å: Chain D: H.77, G.78, D.100, Y.109, Y.113 Ligand excluded by PLIP FMT.31: 4 residues within 4Å: Chain D: P.62, E.63, R.86, Y.87 Ligand excluded by PLIP FMT.32: 4 residues within 4Å: Chain D: A.181, R.208 Chain F: E.54 Ligands: NAP.27 Ligand excluded by PLIP FMT.33: 2 residues within 4Å: Chain D: S.88 Ligands: FMT.38 Ligand excluded by PLIP FMT.34: 4 residues within 4Å: Chain D: R.37, P.76, V.79 Ligands: NAP.27 Ligand excluded by PLIP FMT.35: 3 residues within 4Å: Chain A: D.338 Chain D: G.53, R.54 Ligand excluded by PLIP FMT.36: 4 residues within 4Å: Chain D: E.250, W.254, F.295, E.296 Ligand excluded by PLIP FMT.37: 5 residues within 4Å: Chain D: V.270, K.271, Q.272, R.278, Y.279 Ligand excluded by PLIP FMT.38: 3 residues within 4Å: Chain D: S.88, W.142 Ligands: FMT.33 Ligand excluded by PLIP FMT.39: 2 residues within 4Å: Chain D: L.269, K.271 Ligand excluded by PLIP FMT.41: 6 residues within 4Å: Chain E: N.149, I.177, A.181, Y.202, H.207, A.227 Ligand excluded by PLIP FMT.42: 5 residues within 4Å: Chain E: K.138, N.326, V.327, G.330, W.331 Ligand excluded by PLIP FMT.43: 2 residues within 4Å: Chain E: R.134, E.333 Ligand excluded by PLIP FMT.44: 4 residues within 4Å: Chain E: K.104, V.126, Y.127, Y.133 Ligand excluded by PLIP FMT.45: 6 residues within 4Å: Chain B: P.49 Chain E: V.270, H.277, Y.279, D.281, F.284 Ligand excluded by PLIP FMT.46: 4 residues within 4Å: Chain E: R.283, F.284, L.342, P.344 Ligand excluded by PLIP FMT.47: 7 residues within 4Å: Chain E: P.168, T.169, P.170, I.171, P.221, E.222 Ligands: FMT.50 Ligand excluded by PLIP FMT.48: 5 residues within 4Å: Chain D: E.298 Chain E: Y.112, G.206, H.207, T.210 Ligand excluded by PLIP FMT.49: 4 residues within 4Å: Chain E: Y.133, N.216, L.217, P.218 Ligand excluded by PLIP FMT.50: 5 residues within 4Å: Chain E: L.161, P.168, G.219, P.221 Ligands: FMT.47 Ligand excluded by PLIP FMT.51: 1 residues within 4Å: Chain E: E.222 Ligand excluded by PLIP

2 x ZN: ZINC ION(Non-covalent)

ZN.26: 4 residues within 4Å: Chain C: C.5, C.8, C.25, C.28 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.5, C:C.8, C:C.25, C:C.28 ZN.52: 4 residues within 4Å: Chain F: C.5, C.8, C.25, C.28 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.5, F:C.8, F:C.25, F:C.28

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Shimizu, T. et al., Crystal Structure of the LysYLysW Complex from Thermus thermophilus. J.Biol.Chem. (2016)

Release Date

2016-03-23

Peptides

N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase: ABDE
Alpha-aminoadipate carrier protein LysW: CF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D
A

E
B

C
C

F
C

N-acetyl-gamma-glutamyl-phosphate/N-acetyl-gamma-aminoadipyl-phosphate reductase

Alpha-aminoadipate carrier protein LysW

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